Holly Simon

Holly Simon

Associate Professor
Institute of Environmental Health; Division of Environmental and Biomolecular Systems
Affiliate Scientist, Center for Coastal Margin Observation and Prediction
Office: Hatfield Research Center, 3rd floor, Room 356
Phone: 503-346-3422
Email:
Website: Simon Research Group

Education

B.S., (magna cum laude) Biology/Chemistry, Metropolitan State College of Denver, Colorado
Ph.D., Bacteriology, University of Wisconsin-Madison, 1996

 

Biography

  • University of Wisconsin-Madison, Department of Plant pathology; Research Associate 1996-2000, Assistant Scientist, 2000-2004
  • OHSU/OGI School of Science & Technology, Visiting Assistant Professor, Department of Environmental and Biolecular Systems, 2004

 

Research Interests

Projects in the lab cover a range of topics in microbial ecology, including the study of bacteria and archaea involved in carbon and nitrogen biogeochemical cycles, identification/monitoring of sentinels for environmental change, and remediation of environmental contaminants.

 

Selected Publications

Smith, MW, Davis, RE, Youngblut, NE, Kärnä, T, Herfort, L, Whitaker, RJ, Metcalf, WW, Tebo, BM, Baptista, AM and HM Simon. Metagenomic evidence for reciprocal particle exchange between the mainstem estuary and lateral bay sediments of the lower Columbia River. In revision.

Herfort, L, C Seaton, M Wilkin, B Roman, CM Preston, R Marin III, K Seitz, MW Smith, V Haynes, CA Scholin, AM Baptista, and HM Simon. Use of continuous, real-time observations & model simulations to achieve autonomous, adaptive sampling of microbial processes with a robotic sampler. In revision.

Ghindilis, A.L. Smith M.W., Simon H.M., Seoudi I.A., Yazvenko N.S., Murray I.A., Fu X., Smith K., Jen-Jacobson L., Xu S.-y. (2015). Restriction Cascade Exponential Amplification (RCEA) assay with an attomolar detection limit: a novel, highly specific, isothermal alternative to qPCR. Scientific Reports, 5, 7737; doi:10.1038/srep07737.

Simon, HM, Smith, MW and L Herfort (2014). Tier 2 Focused Review Article:  Metagenomic insights into particles and their associated microbiota in a coastal margin ecosystem. Front. Microbiol., 05 September doi: 10.3389/fmicb.2014.00466.

Smith, MW, Ghindilis, AL, Seoudi, IA, Smith, K, Billharz, R, and HM Simon (2014). A New Restriction Endonuclease-Based Method for Highly-Specific Detection of DNA Targets from Methicillin-Resistant Staphylococcus aureus. PLoS ONE, http://dx.doi.org/10.1371/journal.pone.0097826.

Richard L. Johnson; Christina N. Brow; Reid O'Brien Johnson; Holly M. Simon
Cryogenic core collection and preservation of subsurface samples for biomolecular analysis
Groundwater Monitoring and Remediation. 2013;33(2):38-43.

S.L. Bräuer; K. Kranzler; N. Goodson; D. Murphy; H.M. Simon; A.M. Baptista; B.M. Tebo
Dark Carbon Fixation in the Columbia River's Estuarine Turbidity Maxima: Molecular Characterization of Red-Type cbbL Genes and Measurement of DIC Uptake Rates in Response to Added Electron Donors
Estuaries and Coasts. 2013;36(5):1073-1083.

Maria W. Smith; Lisa Zeigler Allen; Andrew E. Allen; Lydie Herfort; Holly M. Simon
Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem

Frontiers in Microbiology. 2013;4(MAY).

Christina N. Brow; Reid O'Brien Johnson; Richard L. Johnson; Holly M. Simon
Assessment of anaerobic toluene biodegradation activity by bssA transcript/gene ratios
Applied and Environmental Microbiology. 2013;79(17):5338-5344.

Mouzhong Xu; Jon Schnorr; Brandon Keibler; Holly M. Simon
Comparative analysis of 16S rRNA and amoA Genes from archaea selected with organic and inorganic amendments in enrichment culture
Applied and Environmental Microbiology. 2012;78(7):2137-2146.

Andrei L. Ghindilis; Maria W. Smith; Dean S. Messing; Vena N. Haynes; George B. Middleton; Kevin R. Schwarzkopf; Carmen E. Campbell; Changqing Zhan; Bruce Ulrich; Michael J. Frasier; et al.
Development of real-time assays for impedance-based detection of microbial double-stranded DNA targets: Optimization and data analysis
Biosensors and Bioelectronics. 2012;35(1):87-93.

Maria W. Smith; Michelle A. Maier; Dominic Suciu; Tawnya D. Peterson; Tyler Bradstreet; Jordan Nakayama; Holly M. Simon
High resolution microarray assay for rapid taxonomic assessment of Pseudo-nitzschia spp. (Bacillariophyceae) in the field
Harmful Algae. 2012;19:169-180.

S.L. Bräuer; C. Adams; K. Kranzler; D. Murphy; M. Xu; P. Zuber; H.M. Simon; A.M. Baptista; B.M. Tebo
Culturable Rhodobacter and Shewanella species are abundant in estuarine turbidity maxima of the Columbia River
Environmental Microbiology. 2011;13(3):589-603.

Adrin A. Pinto-Tomás; Ana Sittenfeld; Lorena Uribe-Lorío; Felipe Chavarría; Marielos Mora; Daniel H. Janzen; Robert M. Goodman; Holly M. Simon
Comparison of Midgut Bacterial Diversity in Tropical Caterpillars (Lepidoptera: Saturniidae) Fed on Different Diets
Environmental Entomology. 2011;40(5):1111-1122.

Andrey L. Ghindilis; Kevin R. Schwarzkopf; Dean S. Messing; Ibrahim Sezan; Paul Schuele; Changqing Zhan; Maria W. Smith; Holly M. Simon; David R. Evans
Real-time biosensor platform: Fully integrated device for impedimetric assays
ECS Transactions. 2010;33(8):59-68. 
 
Youngblut, N, Wirth, J, Henriksen, J, Smith, MW, Simon, HM, Metcalf, W and R Whitaker,  "Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment" ISME Journal, In press.

Ghindilis, A.L. Smith M.W., Simon H.M., Seoudi I.A., Yazvenko N.S., Murray I.A., Fu X., Smith K., Jen-Jacobson L., Xu S.-y. (2015) Restriction Cascade Exponential Amplification (RCEA) assay with an attomolar detection limit: a novel, highly specific, isothermal alternative to qPCR. Scientific Reports, 5, 7737; doi:10.1038/srep07737. 

Simon, HM, Smith, MW and L Herfort (2014). Tier 2 Focused Review Article:  Metagenomic insights into particles and their associated microbiota in a coastal margin ecosystem. 
Frontiers in Microbiology. 2014;5(SEP).

PLoS ONE. 2014;9(5).